Mercurial > repos > crusoe > khmer
annotate macros.xml @ 21:bc8b334e8f00
indent for pythonic
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 12:30:34 -0400 |
| parents | a3e9ed4bcfdc |
| children | de12b461034f |
| rev | line source |
|---|---|
| 10 | 1 <macros> |
| 2 <xml name="requirements"> | |
| 3 <requirements> | |
| 4 <!-- <requirement type="binary">@BINARY@</requirement> --> | |
| 5 <requirement type="package" version="1.1">khmer</requirement> | |
| 6 </requirements> | |
| 7 <version_command>@BINARY@ --version</version_command> | |
| 8 </xml> | |
| 19 | 9 <token name="@TABLEPARAMS@">#if $parameters.type == "simple" |
| 21 | 10 --ksize=20 |
| 11 --n_tables=4 | |
| 12 --min-tablesize=$parameters.tablesize | |
| 10 | 13 #else |
| 21 | 14 --ksize=$parameters.ksize |
| 15 --n_tables=$parameters.n_tables | |
| 16 --min-tablesize=$parameters.tablesize_specific | |
| 10 | 17 #end if</token> |
| 18 <xml name="tableinputs"> | |
| 19 <conditional name="parameters"> | |
| 20 <param name="type" | |
| 21 type="select" | |
| 22 label="Advanced Parameters" | |
| 13 | 23 help="ksize, n_tables, a specific tablesize" > |
| 10 | 24 <option value="simple" |
| 25 selected="true"> | |
| 26 Hide | |
| 27 </option> | |
| 28 <option value="specific"> | |
| 29 Show | |
| 30 </option> | |
| 31 </param> | |
| 32 <when value="simple"> | |
| 13 | 33 <param name="tablesize" |
| 10 | 34 type="select" |
| 35 label="Sample Type" | |
| 36 display="radio"> | |
| 37 <option value="1e9" | |
| 38 selected="true"> | |
| 39 Microbial Genome | |
| 40 </option> | |
| 41 <option value="2e9"> | |
| 42 Animal Transcriptome | |
| 43 </option> | |
| 44 <option value="4e9"> | |
| 45 Small Animal Genome or Low-Diversity Metagenome | |
| 46 </option> | |
| 47 <option value="16e9"> | |
| 48 Large Animal Genome | |
| 49 </option> | |
| 50 </param> | |
| 51 </when> | |
| 52 <when value="specific"> | |
| 53 <param name="ksize" | |
| 54 type="integer" | |
| 55 value="20" | |
| 56 label="ksize" | |
| 57 help="k-mer size to use" /> | |
| 13 | 58 <param name="n_tables" |
| 10 | 59 type="integer" |
| 60 min="1" | |
| 61 value="4" | |
| 13 | 62 label="n_tables" |
| 63 help="number of tables to use" /> | |
| 16 | 64 <param name="tablesize_specific" |
| 10 | 65 type="text" |
| 13 | 66 label="tablesize" |
| 67 help="lower bound on the tablesize to use" /> | |
| 10 | 68 </when> |
| 69 </conditional> | |
| 70 </xml> | |
|
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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71 <xml name="input_sequences_filenames"> |
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72 <param name="inputs" |
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parents:
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73 multiple="true" |
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74 type="data" |
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75 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" |
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76 label="FAST[AQ] file(s)" |
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cec78b574760
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parents:
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77 help="Put in order of precedence such as longest reads first." /> |
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cec78b574760
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parents:
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changeset
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78 </xml> |
| 10 | 79 <xml name="input_sequence_filename"> |
| 80 <param name="input_sequence_filename" | |
| 81 type="data" | |
| 82 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" | |
| 83 label="FAST[AQ] file(s)" /> | |
| 84 </xml> | |
| 85 <xml name="input_counting_table_filename"> | |
| 86 <param name="input_counting_table_filename" | |
| 87 type="data" | |
| 88 label="the k-mer counting table to query" | |
| 89 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." /> | |
| 90 </xml> | |
| 91 <xml name="abundance-histogram-output"> | |
| 92 <data name="output_histogram_filename" | |
| 93 format="text" | |
| 94 label="${tool.name} k-mer abundance histogram. The | |
| 95 columns are: (1) k-mer abundance, (2) k-mer count, (3) | |
| 96 cumulative count, (4) fraction of total distinct | |
| 97 k-mers."> | |
| 98 </data> | |
| 99 </xml> | |
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parents:
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changeset
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100 <xml name="output_sequences"> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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101 <data name="output" |
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parents:
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102 format="input" |
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cec78b574760
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parents:
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103 label="${tool.name} processed nucleotide sequence file"> |
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cec78b574760
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parents:
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104 <discover_datasets pattern="__name__" directory="output" visible="true"/> |
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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105 </data> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
10
diff
changeset
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106 </xml> |
| 21 | 107 `</macros> |